Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010633.1 Corchorus capsularis cultivar CVL-1 contig10654, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17793
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Found at i:6117 original size:77 final size:80
Alignment explanation
Indices: 5976--6127 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 80
5966 AGTACACAAC
* * *
5976 TAAACACATAGTCTGAAAATAGCATCCACTGCTGAATAATACCACAAACTCCGAATACAAGTACT
1 TAAACACATAGTCTGAAAATAGCA-CAACTACTGAATAACACCACAAACTCCGAATACAAGTACT
6041 GAAT-ATTAACATAAT
65 GAATAATTAACATAAT
* * * * *
6056 TAAACACATTGTCTGAAAAT-GC-CAACTACTGAATGACACCATAAATTCCGAATACAGGTACTG
1 TAAACACATAGTCTGAAAATAGCACAACTACTGAATAACACCACAAACTCCGAATACAAGTACTG
*
6119 CATAATTAA
66 AATAATTAA
6128 ACACATTGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 36 0.58
78 5 0.08
79 2 0.03
80 19 0.31
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (80 bp):
TAAACACATAGTCTGAAAATAGCACAACTACTGAATAACACCACAAACTCCGAATACAAGTACTG
AATAATTAACATAAT
Found at i:9608 original size:14 final size:14
Alignment explanation
Indices: 9589--9615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9579 CTCTCTCTCT
9589 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
9603 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
9616 TATTCAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:9899 original size:28 final size:27
Alignment explanation
Indices: 9804--9901 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 27
9794 TACCTTCTTA
* *
9804 CTTTTTACTGATTAC-CATTT-TACT-
1 CTTTTTACTGATTACTCTTTTCTGCTC
*
9828 C-TTTTACTGATTACTATTTTCTGCTC
1 CTTTTTACTGATTACTCTTTTCTGCTC
9854 CTTTTTTACTGATTACTCTTTTCTGCTC
1 C-TTTTTACTGATTACTCTTTTCTGCTC
9882 CTTTTTCACTGATTACTCTT
1 CTTTTT-ACTGATTACTCTT
9902 GCTTTTTACT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
23 13 0.20
24 4 0.06
25 3 0.05
26 1 0.02
27 5 0.08
28 38 0.59
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.55
Consensus pattern (27 bp):
CTTTTTACTGATTACTCTTTTCTGCTC
Found at i:9954 original size:21 final size:21
Alignment explanation
Indices: 9907--10057 Score: 117
Period size: 21 Copynumber: 6.9 Consensus size: 21
9897 CTCTTGCTTT
9907 TTACTGATTACCT-TTTTACTTC
1 TTACTGATTA-CTATTTTAC-TC
*
9929 TTACTGATTACTATTTTACCC
1 TTACTGATTACTATTTTACTC
* *
9950 TTACTGATTACTATTTATTATTTTT
1 TTACTGATTACTA-TT-TTA--CTC
**
9975 TTACTGGCTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
** * *
9996 TTGTTGATTACCT-TCTTACTTT
1 TTACTGATTA-CTATTTTAC-TC
10018 TTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTC
* *
10039 TTACTAATTACCATTTTAC
1 TTACTGATTACTATTTTAC
10058 CCTTTCAGAT
Statistics
Matches: 101, Mismatches: 20, Indels: 17
0.73 0.14 0.12
Matches are distributed among these distances:
21 48 0.48
22 34 0.34
23 6 0.06
24 2 0.02
25 11 0.11
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (21 bp):
TTACTGATTACTATTTTACTC
Found at i:9959 original size:43 final size:43
Alignment explanation
Indices: 9907--10057 Score: 176
Period size: 43 Copynumber: 3.4 Consensus size: 43
9897 CTCTTGCTTT
* *
9907 TTACTGATTACCTTTTTACTTCTTACTGATTACTATTTTACCC
1 TTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTACTC
* * **
9950 TTACTGATTACTATTTATTATTTTTTTACTGGCTACTATTTTACTC
1 TTACTGATTAC-CTTT-TTA-CTTTTTACTGATTACTATTTTACTC
** *
9996 TTGTTGATTACCTTCTTACTTTTTACTGATTACTATTTTACTC
1 TTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTACTC
* *
10039 TTACTAATTACCATTTTAC
1 TTACTGATTACCTTTTTAC
10058 CCTTTCAGAT
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
43 47 0.54
44 6 0.07
45 5 0.06
46 29 0.33
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (43 bp):
TTACTGATTACCTTTTTACTTTTTACTGATTACTATTTTACTC
Found at i:10299 original size:95 final size:95
Alignment explanation
Indices: 10186--10485 Score: 298
Period size: 95 Copynumber: 3.2 Consensus size: 95
10176 CCTTTCTTAA
*
10186 TTACTGATTACTAATTTTACTCCCTTTTTGATCATCAATTTACTAATTAACCACTCAATTCTTAA
1 TTACTGATTACTAATTTTACTCCCTTTTTAATCATCAATTTACTAATTAACCACTCAATTCTTAA
10251 TTATGATCACTTTAACCCTTAATTATCGAT
66 TTATGATCACTTTAACCCTTAATTATCGAT
* ** * * * * ** *
10281 TTACTGATTACTATTTTTACGTTGACTCTTTAATTA-CAGATTAATCT-CTT-A-C-CTTGACTC
1 TTACTGATTACTAATTTTAC--TCCCTTTTTAATCATCA-ATTTA-CTAATTAACCACTCAATTC
* * ** **
10341 TTTATTA-G-TCCCTTTTGCTTCCTTTCTTA---A-
62 TTAATTATGATCACTTTAAC--CCTTAATTATCGAT
*
10371 TTACTGATTACTAATTTTACTCCCTTTTTTATCATCAATTTACTAATTAACCACTCAATTCTTAA
1 TTACTGATTACTAATTTTACTCCCTTTTTAATCATCAATTTACTAATTAACCACTCAATTCTTAA
10436 TTATGATCACTTTAACCCTTAATTATCGAT
66 TTATGATCACTTTAACCCTTAATTATCGAT
*
10466 TTACTGATTACTATTTTTAC
1 TTACTGATTACTAATTTTAC
10486 GTTGACTCTT
Statistics
Matches: 153, Mismatches: 35, Indels: 34
0.69 0.16 0.15
Matches are distributed among these distances:
87 2 0.01
88 15 0.10
89 3 0.02
90 20 0.13
91 19 0.12
92 8 0.05
93 8 0.05
94 19 0.12
95 39 0.25
96 3 0.02
97 15 0.10
98 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (95 bp):
TTACTGATTACTAATTTTACTCCCTTTTTAATCATCAATTTACTAATTAACCACTCAATTCTTAA
TTATGATCACTTTAACCCTTAATTATCGAT
Found at i:10360 original size:185 final size:185
Alignment explanation
Indices: 10157--10532 Score: 734
Period size: 185 Copynumber: 2.0 Consensus size: 185
10147 CTCTTCTTAC
10157 TTATTAGTCCCTTTTGCTTCCTTTCTTAATTACTGATTACTAATTTTACTCCCTTTTTGATCATC
1 TTATTAGTCCCTTTTGCTTCCTTTCTTAATTACTGATTACTAATTTTACTCCCTTTTTGATCATC
10222 AATTTACTAATTAACCACTCAATTCTTAATTATGATCACTTTAACCCTTAATTATCGATTTACTG
66 AATTTACTAATTAACCACTCAATTCTTAATTATGATCACTTTAACCCTTAATTATCGATTTACTG
10287 ATTACTATTTTTACGTTGACTCTTTAATTACAGATTAATCTCTTACCTTGACTCT
131 ATTACTATTTTTACGTTGACTCTTTAATTACAGATTAATCTCTTACCTTGACTCT
*
10342 TTATTAGTCCCTTTTGCTTCCTTTCTTAATTACTGATTACTAATTTTACTCCCTTTTTTATCATC
1 TTATTAGTCCCTTTTGCTTCCTTTCTTAATTACTGATTACTAATTTTACTCCCTTTTTGATCATC
10407 AATTTACTAATTAACCACTCAATTCTTAATTATGATCACTTTAACCCTTAATTATCGATTTACTG
66 AATTTACTAATTAACCACTCAATTCTTAATTATGATCACTTTAACCCTTAATTATCGATTTACTG
10472 ATTACTATTTTTACGTTGACTCTTTAATTACAGATTAATCTCTTACCTTGACTCT
131 ATTACTATTTTTACGTTGACTCTTTAATTACAGATTAATCTCTTACCTTGACTCT
*
10527 TAATTA
1 TTATTA
10533 TCAATTTACT
Statistics
Matches: 189, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 189 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (185 bp):
TTATTAGTCCCTTTTGCTTCCTTTCTTAATTACTGATTACTAATTTTACTCCCTTTTTGATCATC
AATTTACTAATTAACCACTCAATTCTTAATTATGATCACTTTAACCCTTAATTATCGATTTACTG
ATTACTATTTTTACGTTGACTCTTTAATTACAGATTAATCTCTTACCTTGACTCT
Found at i:10602 original size:55 final size:55
Alignment explanation
Indices: 10541--10845 Score: 440
Period size: 55 Copynumber: 5.8 Consensus size: 55
10531 TATCAATTTA
* * * * *
10541 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTAACT
**
10596 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTAACT
*
10651 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTAACT
10706 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTAC---TACCTTAACT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTAACT
10758 CTGATTAATCTCTTTTTAC----TT--T-A-TTACTGATTAC---TACCTTAACT
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTAACT
10802 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTA
1 CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTA
10846 CCTCTTTTTA
Statistics
Matches: 231, Mismatches: 9, Indels: 21
0.89 0.03 0.08
Matches are distributed among these distances:
44 40 0.17
45 1 0.00
46 1 0.00
48 4 0.02
50 1 0.00
51 1 0.00
52 40 0.17
55 143 0.62
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTAACT
Found at i:10785 original size:44 final size:44
Alignment explanation
Indices: 10737--10833 Score: 194
Period size: 44 Copynumber: 2.2 Consensus size: 44
10727 TATTACTGAT
10737 TTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTA
1 TTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTA
10781 TTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTA
1 TTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTA
10825 TTACTGATT
1 TTACTGATT
10834 TACTGATTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.51
Consensus pattern (44 bp):
TTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTA
Found at i:10851 original size:36 final size:37
Alignment explanation
Indices: 10811--10882 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
10801 TCTGATTAAT
*
10811 CTCTTTTTACTTTATTACTGA-TTTACTGATTACTAC
1 CTCTTTTTACTTAATTACTGATTTTACTGATTACTAC
10847 CTCTTTTTACTTAATTACTGATTTTACTGATTACTA
1 CTCTTTTTACTTAATTACTGATTTTACTGATTACTA
10883 TTACCTTGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 20 0.59
37 14 0.41
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (37 bp):
CTCTTTTTACTTAATTACTGATTTTACTGATTACTAC
Found at i:10880 original size:96 final size:93
Alignment explanation
Indices: 10674--10925 Score: 300
Period size: 96 Copynumber: 2.6 Consensus size: 93
10664 TTTTACTTAA
10674 TTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGATTT
1 TTACTGA-TTACTGATTAC---TACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGATTT
10739 ACTGATTACTACCTTAACTCTGATTAATCTCTTT
62 ACTGATTACTACCTT-A-TCTGATTAATCTCTTT
*
10773 TTACTTTATTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGATTTACT
1 TTAC-TGATTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGATTTACT
* *
10838 GATTACTACCTCT-TTTTACTTAAT-TACTGATT
65 GATTACTACCT-TATCTGA-TTAATCT-CT--TT
** *
10870 TTACTGATTACT-A-T--TACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTGATT
1 TTACTGATTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGATT
10926 GCCCTTTTTT
Statistics
Matches: 140, Mismatches: 7, Indels: 19
0.84 0.04 0.11
Matches are distributed among these distances:
92 39 0.28
94 5 0.04
95 8 0.06
96 64 0.46
97 7 0.05
99 15 0.11
100 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.51
Consensus pattern (93 bp):
TTACTGATTACTGATTACTACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGATTTACTG
ATTACTACCTTATCTGATTAATCTCTTT
Found at i:11750 original size:51 final size:50
Alignment explanation
Indices: 11620--11821 Score: 212
Period size: 50 Copynumber: 4.1 Consensus size: 50
11610 AACTAATCAA
** * * * * *
11620 TTTATTTACTAATGGCCTAAAAGTTCAAACTTCTAATTCAAAGGCGACAT-
1 TTTATTTACTAATTACTTAAAAATTCAATCTT-TTATTCAAAGGTGACATC
* * *
11670 TTTATTTACTAA--ACTTAAAAATTCTATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
** * * *
11718 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCTAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTGACATC
* *
11769 TTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
11819 TTT
1 TTT
11822 TAGCCAAATA
Statistics
Matches: 124, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
47 13 0.10
48 25 0.20
50 45 0.36
51 41 0.33
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTGACATC
Found at i:11823 original size:51 final size:51
Alignment explanation
Indices: 11620--11823 Score: 204
Period size: 51 Copynumber: 4.1 Consensus size: 51
11610 AACTAATCAA
** * * * * **
11620 TTTATTTACTAATGGCCTAAAAGTTCAAACTTCTAATTCAAAGGCGACA--T
1 TTTATTTACTAATTACTTAAAAATTCAATCTT-TTATTCAAAGGTTACATCT
* *
11670 TTTATTTACTAA--ACTTAAAAATTCTATCTTTTATTCAAAGGTTAAATC-
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
** * * *
11718 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTACCCTAAGATGACAT-T
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTACATCT
*
11769 TTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
11820 TTTA
1 TTTA
11824 GCCAAATATC
Statistics
Matches: 125, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
47 12 0.10
48 25 0.20
50 42 0.34
51 46 0.37
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (51 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
Found at i:14649 original size:27 final size:27
Alignment explanation
Indices: 14619--14694 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
14609 AGGTGAACTT
* *
14619 AAAAATAACTAAAATGTCCC-TGAGTGC
1 AAAAATGACCAAAATG-CCCTTGAGTGC
*
14646 AAAAATGACCAAAATGCCCTTGGGTGC
1 AAAAATGACCAAAATGCCCTTGAGTGC
*
14673 AAAAATGACCAAAATACCCTTG
1 AAAAATGACCAAAATGCCCTTG
14695 GGCGGCCCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCTTGAGTGC
Found at i:14695 original size:27 final size:27
Alignment explanation
Indices: 14642--14696 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
14632 ATGTCCCTGA
*
14642 GTGCAAAAATGACCAAAATGCCCTTGG
1 GTGCAAAAATGACCAAAATACCCTTGG
14669 GTGCAAAAATGACCAAAATACCCTTGG
1 GTGCAAAAATGACCAAAATACCCTTGG
14696 G
1 G
14697 CGGCCCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (27 bp):
GTGCAAAAATGACCAAAATACCCTTGG
Found at i:14995 original size:33 final size:33
Alignment explanation
Indices: 14953--15039 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
14943 GGATCGTGTG
*
14953 GCCGGTTGTGGTCGGGCATGGCCGAGCCATGTT
1 GCCGGTTGTGGCCGGGCATGGCCGAGCCATGTT
14986 GCCGGTTGTGGCCGGGCATGGCCGAGCCATGTT
1 GCCGGTTGTGGCCGGGCATGGCCGAGCCATGTT
15019 GCCGGTTGTGGCCGGGCATGG
1 GCCGGTTGTGGCCGGGCATGG
15040 TCATGTCGCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.08, C:0.25, G:0.45, T:0.22
Consensus pattern (33 bp):
GCCGGTTGTGGCCGGGCATGGCCGAGCCATGTT
Done.